What we do

The Molecular Modelling Group studies molecular interactions using modelling techniques such as homology modelling, molecular dynamics, docking and free energy simulations. Our main activity consists in developing and applying methods for computer-aided protein engineering and drug design. Notably, we develop novel inhibitors of important targets for cancer therapy and design optimized proteins, such as T-cell receptors, for cancer immunotherapy. We develop and maintain web tools for drug design, such as SwissDock, SwissTargetPrediction and SwissADME. We also run the Protein Modelling Facility of the University of Lausanne (UNIL).

Highlights 2017

In 2017, the group released SwissADME, a new web tool to compute the physicochemistry and estimate the pharmacokinetics, druglikeness and medicinal chemistry friendliness of small molecules. Among others, SwissADME provides an exclusive access to our in-house models iLogP and BOILED-Egg. The SwissADME interface was designed for both experts and non-experts. SwissADME is part of a large SIB initiative to provide online tools for drug design – such as SwissDock, SwissBioisostere, SwissTargetPrediction and SwissSimilarity, with which it can interoperate. The group continued the development of a new on-the-fly QM/MM docking algorithm within the in-house docking tool Attracting Cavities, and of a novel approach for automated structure-based ligand design, SwissGrowing. We also started the development of a new web-based tool for Personalized Oncology, which aims to facilitate the prediction of the effect of cancer-cell mutations that have not yet been characterized experimentally.

Find out more about the Group’s activities

Main publications 2017

  • Daina A et al. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717.
  • Chaskar P et al. On-the-Fly QM/MM Docking with Attracting Cavities. J Chem Inf Model. 2017;57(1):73-84.
  • Röhrig UF et al. The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1). Biochemistry. 2017;56(33):4323-4325.